[gmx-users] System blowing up - equilibration step - CG simulation

[Carlos Navarro Retamal]

Dear Gromacs users,
I'm trying to perform a CG simulations of a system consisting in a protein locate at 5 nm with respect to the charged groups of a MGDG membrane.
I first performed an EM in vaccum.
After that, to constructed the system i use insane.py as following:
./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5 -box 10,10,10 -l MGDG -sol W -orient

Later, i ran a EM with the whole system, with the respective output:
Steepest Descents converged to machine precision in 2081 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.6833109e+05
Maximum force = 3.5193942e+02 on atom 3598
Norm of force = 6.2432761e+00,

Sadly, when i'm trying to perform an equilibration i got the following error message:
Step 10:
Atom 8449 moved more than the distance allowed by the domain decomposition (1.590000) in direction Z
distance out of cell 1330.886108
Old coordinates: 1.667 4.809 0.710
New coordinates: -1840.027 -454.814 1335.667
Old cell boundaries in direction Z: 0.000 5.000
New cell boundaries in direction Z: 0.000 4.781
________________________________
Program mdrun, VERSION 5.0.4
Source code file: /home/krlitros87/Downloads/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 4390

Fatal error:
An atom moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors<http://www.gromacs.org/Documentation/Errors>


This is the .mdp file:
define = -DPOSRES
dt = 0.02
cutoff-scheme = group
nsteps = 500000
nstxout = 0
nstvout = 0
nstlog = 100
nstxtcout = 100
xtc-precision = 10
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = Berendsen
tc-grps = Protein MGDG W ION
tau-t = 1.0 1.0 1.0 1.0
ref-t = 323 323 323 323
Pcoupl = Berendsen
Pcoupltype = isotropic
tau-p = 5.0
compressibility = 3e-4
ref-p = 1.0
refcoord_scaling = all

I know that my system is blowing up, but what can i do to avoid this issue? I tried increasing the EM step without luck.
If you need more info related my problem please let me know.
Hope someone can help me.
Best regards,
Carlos

--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl